Characterization of chromatin remodelers and epigenetic factors in blood cell development

How a single cell can divide and differentiate into an entire organism is of immense intrigue to me. In an organism, cells, tissues and organs work in concert for normal development, perturbation of which causes developmental disorders and disease. My laboratory is interested to find out the contribution of chromatin remodeling complexes and their subunits towards development and diseases of the human hematopoietic system.

Chromatin and chromatin remodelers

The highly compacted eukaryotic genome is composed of nucleosomes as its basic unit. Nucleosomes are composed of 147 bp of DNA wrapped around an octameric core of histone proteins. To make DNA accessible for factors regulating biological processes, cells possess enzymes called ATP-dependent chromatin remodeling complexes (CRCs). These enzymes utilize the energy of ATP hydrolysis to remodel chromatin. CRCs belong to the SNF2 family of ATPases and have been classified into subfamilies based on the presence of different domains, other than the ATPase domain present in the catalytic subunit. The four families of CRCs are SWI/SNF (SWItch/Sucrose Non-fermenting), ISWI (Imitation Switch), CHD (Chromodomain helicase DNA binding proteins)and INO80/SWR1. CRCs, which are usually multisubunit enzyme complexes, possess several domains in its ATPase and auxiliary subunits, which interpret epigenetic codes residing on histone tails, thereby determining the fate of chromatin and gene expression.

Decades of research from various laboratories have shown that CRCs have distinct and redundant ways to change chromatin architecture, namely, by nucleosome assembly, sliding, spacing and eviction, dimer displacement and change of nucleosome composition with histone variants. To add another level of complexity, CRCs have tissue-specific or developmental stage specific isoforms, which determines the development or lineage commitment of the tissue/cell type in question. In other words, a combinatorial association of auxiliary subunits can define the lineage choice. Impaired function of CRCs has been implicated in developmental disorders and cancer.

Mammalian hematopoiesis

In hematopoiesis, various types of blood cells are produced from hematopoietic stem cells (HSCs) in the bone marrow. Hematopoietic differentiation can be broadly categorized into two major lineages; lymphoid and myeloid lineages. Lymphoid lineage gives rise to mature B cells, T cells, and natural killer cells and the myeloid lineage give rise to granulocytes, (consisting of neutrophils, basophils, eosinophils) monocytes, macrophages, megakaryocytes, platelets, and erythrocytes.

Differentiation block in myeloid progenitors results in an abnormal clonal expansion of myeloid blast cells in peripheral blood and in bone marrow. The blast cells fail to undergo normal maturation process to produce different kinds of normal myeloid cells and result in a population of myeloid blasts. Myeloid blasts or leukemic blasts over populate normal myeloid cells thereby compromising an individual’s normal blood homeostasis. Such abnormalities in myeloid differentiation result in myeloid malignancies called Acute Myeloid Leukemia (AML). AML is a heterogeneous disease that consists of several subtypes based on cytogenetic and genetic alterations, which is also the basis for classification and prognosis. AML is characterized by disturbed transcriptional regulation that leads to a differentiation block and increased proliferation. To determine the abnormalities in AML, it is, therefore, important to understand normal myelopoiesis.

The research interest of the lab is identification and characterization of different chromatin remodelers and their subunits towards development and diseases of the human hematopoietic system. We are specifically interested in understanding myeloid development/differentiation program and how impairment in gene expression results in myeloid disorders. We use molecular biology, biochemistry, and next-generation sequencing approaches to understand how chromatin remodelers regulate chromatin architecture which in turn regulate gene expression for myeloid lineage choice and differentiation.

Publications

1. Prasad, P., Mahapatra, S., Mishra, R., et al. Long-read 16S-seq reveals nasopharynx microbial dysbiosis and enrichment of Mycobacterium and Mycoplasma in COVID-19 patients: A potential source of co-infection. Mol Omics (2022). DOI: 10.1039/d2mo00044j.
2. Saha, S. et al. SMARCD1 negatively regulates myeloid differentiation of leukemic cells via epigenetic mechanisms. Blood Adv, doi:10.1182/bloodadvances.2021006235 (2022).
3. Suresh, V. et al. Quantitative proteomics of hamster lung tissues infected with SARS-CoV-2 reveal host factors having implication in the disease pathogenesis and severity. FASEB J 35, e21713, doi:10.1096/fj.202100431R (2021).
4. Shriwas, O. et al. RRBP1 rewires cisplatin resistance in oral squamous cell carcinoma by regulating Hippo pathway. Br J Cancer, doi:10.1038/s41416-021-01336-7 (2021).
5. Sethi, M. et al. Targeted (PCR-based) screening of antibiotic resistance genes’ prevalence in the gut microbiota of tribal people of Nabarangpur, Odisha, India. Lett Appl Microbiol, doi:10.1111/lam.13642 (2021).
6. Nath, P. et al. Inhibition of IRGM establishes a robust antiviral immune state to restrict pathogenic viruses. EMBO Rep 22, e52948, doi:10.15252/embr.202152948 (2021).
7. Mlcochova, P. et al. SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion. Nature 599, 114-119, doi:10.1038/s41586-021-03944-y (2021).
8. Dong, W., Prasad, P., Lennartsson, A. & Ekwall, K. The Role of Non-Catalytic Domains of Hrp3 in Nucleosome Remodeling. International journal of molecular sciences 22, 1793 (2021).
9. Dhar, M. S. et al. Genomic characterization and epidemiology of an emerging SARS-CoV-2 variant in Delhi, India. Science 374, 995-999, doi:10.1126/science.abj9932 (2021).
10. Raghav S, Ghosh A, ….Prasad P..et. al. Analysis of Indian SARS-CoV-2 Genomes Reveals Prevalence of D614G Mutation in Spike Protein Predicting an Increase in Interaction With TMPRSS2 and Virus Infectivity. Frontiers in microbiology, 11, p2847, 2020
11. Jena K*, Mehto S*, Nath P*, Chauhan NR, Sahu R, Dhar K, Das SK, Kolapalli SP, Murmu KC, Jain A, Krishna S, Sahoo BS, Chattopadhyay S, Rusten TE, Prasad P, Chauhan S, Santosh Chauhan**Autoimmunity gene IRGM suppresses cGAS‐STING and RIG‐I‐MAVS signaling to control interferon response. EMBO Rep (2020)e50051 https://doi.org/10.15252/embr.202050051
12. Dong W, Oya E, Zahedi Y, Prasad P, Svensson JP, Lennartsson A, Ekwall K, Durand-Dubief M: Abo1 is required for the H3K9me2 to H3K9me3 transition in heterochromatin. Scientific reports 2020, 10(1):1-13. 
    
13. Subha Saha†, Krushna Chandra Murmu†, Mayukh Biswas, Sohini Chakraborty, Jhinuk Basu, Swati Madhulika, Srinivasa Prasad Kolapalli, Santosh Chauhan, Amitava Sengupta and Punit Prasad*. Transcriptomic Analysis Identifies RNA Binding Proteins as Putative Regulators of Myelopoiesis and Leukemia. (2019) Frontiers in Oncology. August 2019, Volume 9, Article 692 p1-15.
14. Sadeghi L, Prasad P, Ekwall K, Cohen A, Svensson JP. The Paf1 complex factors Leo1 and Paf1 promote local histone turnover to modulate chromatin states in fission yeast (2015). EMBO Rep. Dec; 16(12):1673-87. doi:10.15252/embr.201541214.
15. Prasad P*, Rönnerblad M*, Arner E, Itoh M, Kawaji H, Lassmann T, Daub C, Alistair R.R. Forrest, Lennartsson A and Ekwall K. High-throughput transcription profiling identifies putative epigenetic regulators of hematopoiesis. (2014) Blood. Apr24; 123(17): e46-57 (*Co-first authors)
    • Comment on Prasad al. article in Deep sequencing blood transcriptomes by Forrest AR. Blood. 2014 Apr 24;123(17):2595-6. PMID:24764555
    • Cited in Top Stories in ‘Hematopoiesis News’ volume 5-12, Apr1 2014 (http://www.hematopoiesisnews.com/issue/volume-5-12-apr-1/)
16. Norman-Axelsson U, Durand-Dubief M, Prasad P and Karl Ekwall. DNA topoisomerase III localizes to centromeres and affects centromeric CENP-A levels in fission yeast. (2013) PloS Genetics Mar 14 9(3).
17. Deindl S, Hwang WL, Hota SK, Blosser TR, Prasad P, Bartholomew B, Zhuang X. ISWI Remodelers Slide Nucleosomes with Coordinated Multi-Base-Pair Entry Steps and Single-Base-Pair Exit Steps. (2013) Cell. Jan 31;152(3):442-52. PMID: 23374341
18. Pointner J*, Persson P*, Prasad P*, Norman U, Strålfors A, Khorosjutina O, Krietenstein N, Ekwall K, and Korber P. CHD1 remodelers space nucleosomes in vitro and link regular arrays to 5’ ends of genes in S. pombe. (2012) EMBO J. Nov 28,31(23):4388-403. (*Co- first authors).
    • Comment on Pointner, Persson, Prasad al. Nucleosome positioning and transcription: fission yeast CHD remodellers make their move by Touat-Todeschini et. al. EMBO J. 2012 Nov 28;31(23):4371-2. PMID: 23103764
19. Dechassa ML, Hota SK, Sen P, Chatterjee N, Prasad P, Bartholomew B. Disparity in theDNA translocase domains of SWI/SNF and ISW2. (2012) Nucleic Acids Res. May;40(10):4412-21.
20. Gangaraju VK*, Prasad P*, Srour A, Kagalwala MN, Bartholomew B. Conformationalchanges associated with template commitment in ATP-dependent chromatin remodeling by ISW2. (2009). Mol Cell. Jul 10; 35(1):58-69. (*Co-first authors).

 Book Chapters

1. Hota SK, Dechassa ML, Prasad P, Bartholomew B. Mapping protein-DNA and protein- protein interactions of ATP-dependent chromatin remodelers. (2012). Methods Mol Biol. 809:381-409.

 Reviews

1. Prasad P*, Lennartsson A and Ekwall K*. The roles of SNF2/SWI2 nucleosome remodeling enzymes in blood cell differentiation and leukemia. (2015) BioMed Research International Feb 19, 2015 Article ID 347571. (*Co-corresponding author)
2. Prasad P, Ekwall K. A snapshot of Snf2 enzymes in fission yeast. Biochem Soc Trans. 2013 Dec 1;41(6):1640-7.
3. Prasad P, Ekwall K. New insights into how chromatin remodelers direct CENP-A to centromeres. (2011) EMBO J. May 18; 30(10):1875-6.
4. Prasad P, Bartholomew B. Control of nucleosome movement: to space or not to space nucleosomes? (2010) Epigenetics. May 16; 5(4):282-6.

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Past Lab members:

1. Laboratory Technician: Ms. Pritina Samal

2. DBT-RA: Devyani Samantarrai, PhD

3. DBT-RA: Sarbani Ashe

4. Venkateswarlu Perikala, RA

5. Laboratory Manager : Subhabrata Barik

Summer Trainees

1. Ms. Chitresha Pal pursuing M.Sc. in Genomics at Central University of Kerala (May-June 2018)

2. Ms. Ankita Mohanty pursuing B.Tech-M.Tech at KIIT (May-June 2018; Dec-May 2019)

3. Ms. Stella Sahu pursuing M.Sc in Bioinformatics at OUAT (Mar-July 2018)

4. Ms. Mamta Rathore, KARYA fellow, Dept. of Science and Technology, Rajasthan (Aug-Sept 2018)

5. Ms. Bhumika Maharana pursuing B.Tech-M.Tech at KIIT (May-June 2019)

6. Ms. Pratikshya Panda pursuing B.Tech-M.Tech at KIIT (May-June 2019)

7. Ms. Ishani Panda pursuing M.Sc. in Genomics at Central University of Kerala (May-June 2019)

8. Mr. Ankit Singh pursuing BS-MS Dual degree from IISER Bhopal (May-June 2019)

Generous intramural start-up support from ILS

Ramalingaswami Fellowship – 2016

SERB EMR – 2019-2022

ICMR – 2022-2025

My lab is actively looking for prospective enthusiastic Post Doctoral fellows, who are interested in the field of chromatin remodeling, epigenetics and hematopoiesis. Scholars who have finished/finishing their Ph.D. are encouraged to apply with their detailed CV and one to two pages write-up describing their research interests. Candidates with experience in molecular biology, cell biology and bioinformatics will be preferred. The applicants should have postdoctoral fellowship or willing to apply for the fellowship. I will be happy to guide prospective candidates through the research proposal and application process for obtaining Postdoc fellowships.

Vacancy for a SRF position under SERB EMR (2019-2022) project for three years. Looking for a person with strong bioinformatics background and knowledge of biological sciences.

Interested candidates should contact me at punitprasad.ils@gmail.com; punit@ils.res.in